PMID: 11921442Mar 29, 2002Paper

A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis

Proteomics
Jan Eriksson, David Fenyö

Abstract

A rapid and accurate method for testing the significance of protein identities determined by mass spectrometric analysis of protein digests and genome database searching is presented. The method is based on direct computation using a statistical model of the random matching of measured and theoretical proteolytic peptide masses. Protein identification algorithms typically rank the proteins of a genome database according to a score based on the number of matches between the masses obtained by mass spectrometry analysis and the theoretical proteolytic peptide masses of a database protein. The random matching of experimental and theoretical masses can cause false results. A result is significant only if the score characterizing the result deviates significantly from the score expected from a false result. A distribution of the score (number of matches) for random (false) results is computed directly from our model of the random matching, which allows significance testing under any experimental and database search constraints. In order to mimic protein identification data quality in large-scale proteome projects, low-to-high quality proteolytic peptide mass data were generated in silico and subsequently submitted to a database sear...Continue Reading

Citations

Sep 5, 2003·Journal of the American Society for Mass Spectrometry·William J HenzelJohn T Stults
Jul 26, 2007·Chemical Reviews·Tao LiuRichard D Smith
Jun 27, 2009·Molecular & Cellular Proteomics : MCP·Jamie ShermanMark P Molloy
Jan 13, 2006·Omics : a Journal of Integrative Biology·Tema FridmanAndrey Gorin
Oct 15, 2003·Rapid Communications in Mass Spectrometry : RCM·Robertson Craig, Ronald C Beavis
Jul 19, 2002·Journal of Mass Spectrometry : JMS
Jul 2, 2003·Molecular & Cellular Proteomics : MCP·Nükhet CavusogluThierry Léveillard
Mar 6, 2004·Journal of Animal Science·L G Sheffield, J J Gavinski
Apr 13, 2005·Journal of Proteome Research·Jan Eriksson, David Fenyö

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.